SBMLWebApp

SBMLWebApp provides computational analysis of systems biology models encoded in the Systems Biology Markup Language (SBML), enabling dynamic ODE simulation, steady-state analysis, and parameter estimation for model-based investigation.

Key Features:

• Dynamic Simulation: Performs time-course simulations of SBML models defined by ordinary differential equations (ODEs).
• Steady-State Analysis: Computes system equilibria and analyzes stability for SBML-encoded networks.
• Parameter Estimation: Fits model parameters to experimental data to refine model predictions.
• Direct Model Access: Imports SBML models directly from the BioModels Database for immediate analysis.

Scientific Applications:

• Model Validation and Refinement: Validate model behavior against experimental data and refine parameters to improve model accuracy.
• Hypothesis Testing: Evaluate system responses to parameter changes or perturbations using simulation and steady-state analyses.
• Educational Purposes: Illustrate ODE-based systems biology modeling and analysis for training and coursework.

Methodology:

Implemented in Java on an Apache Tomcat web server and uses COPASI, SBSCL, and LibSBMLSim as simulation engines to execute dynamic simulations, steady-state analyses, and parameter estimation on SBML models.